The top scorer at the 1966 Cup also urged the media and public not to be too hard on England's Wayne Rooney and Portugal's Cristiano Ronaldo, who he said had tried but failed to reach their full potential in South Africa.
Eusebio and Germany's Gerd Muller, Golden Boot winner at the 1970 World Cup, picked Argentina striker Gonzalo Higuain, Spain's David Villa and Thomas Muller of Germany to fight it out for the 2010 top scorer award.
But for Eusebio, Messi is the star.
"I have no doubt that this little player who happens to be Argentinean, Messi, will be the best player of this tournament," he told reporters in Johannesburg.
FIFA World Player of the Year Messi is still waiting for his first goal in the competition but has played brilliantly, coming close repeatedly and setting up his teammates while helping his country canter through to the quarter-finals.
A rejuvenated Argentina, after a poor qualifying campaign, face Germany in the last eight on Friday. The Golden Boot is awarded to the top goalscorer while the Golden Ball goes to the best player.
BRAZIL TO WIN
Eusebio picked Brazil to win their sixth trophy, but was less sure which team would challenge them in the final, and shied away from criticising compatriot Ronaldo for a less than convincing tournament.
"Unfortunately for Portugal, Cristiano Ronaldo did not do very well in this championship, but I am not going to condemn him for that," he said.
"I have also played in the past and I can understand players are in good or bad form."
Portugal lost to Spain in the second round, with Ronaldo, World Player of the Year in 2008, scoring just one goal which came during the team's 7-0 rout of North Korea.
However, Eusebio said his country were unlucky not to made it through to the quarter-finals.
"I believe Portugal played very well, we were beaten by Spain, by 1-0, and a very doubtful goal," he said.
Villa scored the winner for Spain, which some Portuguese players said should have been disallowed for offside.
Eusebio also defended Brazil's Kaka for being sent off against Ivory Coast for a second yellow card after allegedly elbowing Abdelkader Keita, saying he fell foul of the antics of other players and a "sleeping" linesman.
"I know Kaka very well, he is a true professional ... in this particular case I saw Kaka being provoked by the other player, I didn't see him touch the other player," he said.
"What I believe also is that maybe the linesman shouldn't fall asleep."
